Satellite Repeats in genome assemblies

lh3 / srf

SRF: Satellite Repeat Finder

MIT License

87 stars 6 forks source link

Satellite Repeats in genome assemblies #4

Closed sanyalab closed 1 year ago

sanyalab commented 1 year ago

Hello,

I have High-quality genome assemblies in a weed species. Can this tool be used to identify HOR's and other satellite repeats in whole genome assemblies?

Thanks

lh3 commented 1 year ago

SRF works with assemblies, provided that it is a HiFi or duplex assembly assembled by hifiasm, verkko, HiCanu or LJA. Most other assemblers will collapse satellites.